March 09, 2011

Out of South Africa? Out of anywhere?

The most widely circulated theory of modern human origins involves the emergence of our species from a small tribe of only a few thousand people who lived in East Africa. There are three main arguments in favor of this theory:

The earliest anatomically modern (albeit with archaic traits) skulls are found in Ethiopia (Omo skulls, dated to 195 thousand years ago)

The shallow coalescence times of human mtDNA and Y-chromosomes (within the last 200 thousand years) is seen as evidence for a recent emergence of our species.

Diminution of genetic diversity across Eurasia is proportional to distance from East Africa

Of course, there are counter-arguments for all these claims:

Modern human skulls may have been preserved in Ethiopia because of its climate which is favorable to preservation and/or the extreme interest by palaeoanthropologists on this region

The shallow coalescence times may be the result of selective sweeps affecting these uniparental markers and do not, in general have much to say about the time depth of the species. Anyway, the molecular dates are highly suspect, not to mention that other genetic systems are supportive of more complex processes than the recent Out of Africa model popularized in the media.

Diminution of genetic diversity across Eurasia tells us nothing about how genetic diversity is distributed within Africa itself. Indeed:

We would expect the exit of modern humans to occur in East Africa irrespective of whether they originated there or not: decreased genetic diversity with distance from east Africa simply means that Eurasians may have passed through east Africa, not that they originated there.

The law-like diminution of genetic diversity from east Africa is questionable

The paper that is the subject of this post shows that within Africa east Africans are not the most genetically diverse

The most scathing criticism of the east African, or, indeed, any single origin of mankind comes frommultiregional evolution (MRE). This theory, seen in a more favorable light after ancient DNA research's 2 for 2 record of inferring archaic admixture in modern humans questions the very idea of an "origin" of humans in some small geographically circumscribed place.

Rather, it proposes that modern humans (Homo sapiens) are genomic blends of components that originated at different times in different places: there was never an "African tribe on the verge of extinction that went on to populate the world", but a single set of interbreeding Homo populations where alleles could (and did) originate anywhere, and:

the reduced overall diversity within our species is not due to a bottleneck but to the culling of variation by natural selection, although not of the classical sweep kind.

The current paper argues against and east African origin of mankind and in favor of a south African one. I can't help but feel the irony of the fact that recently north Africawas implicated in modern human origins, while just yesterday I posted an abstract from the upcoming AAPA 2011 which rejects a south African origin and favors higher central/east African genetic diversity (at least for the Y-chromosome)!

Things are clearly not simple.

What is the underlying assumption causing so many divergent opinions? I would say it is the phylogeographic axiom that greater diversity implies place of origin. This is made explicit by an author of the paper in the following quote:

Henn admits that migration could certainly be a possibility, but counters that when a population migrates, typically only a subset moves to a new area, and this subset is less genetically diverse than the parent population. She argues that if a group left eastern African for southern Africa it would be expected to have less diversity in the south. "This is not what we find in the data," she says.

True, but this tree-like model of human migration does not really capture the complexity of what happened. Because a population's diversity does not increase only when it is ancient, but also when it is admixed, the product of the coming together of two genetically divergent populations. Indeed, within the paper itself can be found this statement:

Recently Tishkoff et al. (3) suggested a potential origin for modern humans in southern Africa, on the basis of heterozygosity estimates from microsatellite data. However, their sample of KhoeSan was small, and the directionality of a southwestern origin of humans based on heterozygosity could have been driven by the inclusion of a highly admixed (and thus highly heterozygous) “Coloured” population.

But, the same could very well be true for the highly diverse KhoeSan population of African hunter-gatherers! Their greater genetic diversity could mean they are highly admixed, rather than they are very old.

There is, however, an additional argument, based on patterns of linkage disequilibrium. Typically admixed individuals have high LD, as they inherit whole blocks of DNA from one or the other of the source populations. LD decays over time. A recently admixed population is expected to have high LD. Yet, it may very well be the case that the very low LD observed in the KhoeSan may be compatible with their status as an admixed population if the admixture event took place long ago.

Readers of the blog know that this is precisely what I have proposed: that African hunter-gatherers are to a large extent the product of old admixture between "modern" humans and archaic Africans, just as Eurasians may also be the product old admixture between "modern" humans and archaic Eurasians, such as the Neandertals or Denisovans.

Old admixture implies non-tree-like evolution and invalidates the aforementioned phylogeographic axiom. It implies that places of high diversity may be due to admixture, and not to antiquity.

In any case, while I don't believe that this paper proves the south African origin of mankind, it is an extremely important contribution to the sampling of African genomic diversity, and hopefully its data will be useful in the future, and I don't doubt that I will find some use of the ~55K SNPs for several populations in my Dodecad Project.

Africa is inferred to be the continent of origin for all modern human populations, but the details of human prehistory and evolution in Africa remain largely obscure owing to the complex histories of hundreds of distinct populations. We present data for more than 580,000 SNPs for several hunter-gatherer populations: the Hadza and Sandawe of Tanzania, and the ≠Khomani Bushmen of South Africa, including speakers of the nearly extinct N|u language. We find that African hunter-gatherer populations today remain highly differentiated, encompassing major components of variation that are not found in other African populations. Hunter-gatherer populations also tend to have the lowest levels of genome-wide linkage disequilibrium among 27 African populations. We analyzed geographic patterns of linkage disequilibrium and population differentiation, as measured by FST, in Africa. The observed patterns are consistent with an origin of modern humans in southern Africa rather than eastern Africa, as is generally assumed. Additionally, genetic variation in African hunter-gatherer populations has been significantly affected by interaction with farmers and herders over the past 5,000 y, through both severe population bottlenecks and sex-biased migration. However, African hunter-gatherer populations continue to maintain the highest levels of genetic diversity in the world.

6 comments:

Regarding the genetic diversity of the San people, it is worth mentioning that their highly divergent Y-DNA and mtDNA suggests that they did branch off from the ancestors of most other human groups pretty early on, and this would also explain their greater diversity.

It is interesting to see the small Tuscan component (orange color) scattered throughout some of the African samples. I wonder if that can be associated with E1b1b(1)M215/ M35?

The seeming Bantu component (rusty red color) is not surprising...

The small, but interesting San component (sky blue color) in the Biaka Pygmy, Mandenka, and Yoruba...What do you make of that, Dienekes? The others with that very small component are not too surprising because of contacts with click-speaking populations. The Yoruba, Mandenka, and Biaka Pygmies are different because of location, well away from click-speaking populations.

The tiny Maasai component (yellow and pink colors) in the Mandenka and Yoruba...interesting also. Same with the Hadza and Sandawe component in those two populations...The yellow and pink color seem to be most strongly assocoated with Nilo-Saharan speakers (the Maasai).

There seems to have been a small amount of gene flow from East to West???

"It is interesting to see the small Tuscan component (orange color) scattered throughout some of the African samples. I wonder if that can be associated with E1b1b(1)M215/ M35?"

In the case of the South African San samples, it is certainly due to the European colonization and recent European admixture, as is also clear from the MDS results of the South African San samples and the Admixture and MDS results of the Namibian San samples, who all clearly lack European admixture.

Greater genetic diversity does imply a more ancient population from which other less ancient populations have budded off. Of course all humans are of the same age, I am referring to populations of humans.

Africans, sub Saharan, are seem as comprising the most ancient human populations and Europeans less ancient. That is fair enough. The problem is that when it comes to Southern Europeans it is believed that their greater genetic diversity is due to admixture and that the lower genetic diversity found in Northern Europeans is due to Northern Europeans been purer, unmixed and more autochthonous European.

It is either one or the other. Greater genetic diversity means a more ancient population or higher admixture. Well test each hypothesis. Mexicans are a good example to use as they come from an admixed population and from one derived from immigrants from North east Asia which underwent a bottleneck, and had less diversity to start with.

The admixed status of Mexicans can be inferred because there still exist in unadmixed form the constituent elements that led to their formation, and the admixture event took place recently enough for entire blocks of DNA to be inherited in them from definite continental sources.

The case of Africans is quite interesting in that respect. If the Bushmen hadn't been discovered for a thousand years more, chances are they would've been totally assimilated by the Bantu and it would've been impossible to infer their very existence, unless one dug up some of their bones, DNA tested them, and noticed that a few modern humans resemble them more.

In all likelihood, the farming dispersal in Africa, as well as the spread of modern humans much earlier led to the assimilation of numerous tribes of "Palaeoafricans" whose diversity cannot be measured, because they no longer exist as distinct people. The fact that the Bushmen have the highest genetic diversity does not mean that modern humans originated there: the (more? less?) diverse DNA of other Palaeoafrican tribes assimilated by farmers/pastoralists emanating from different parts of Africa simple no longer exists in a distinct people, but only as assimilated bits in the demographically dominant (and genetically homogeneous) gene pool of the dominant groups.

"Rather, it proposes that modern humans (Homo sapiens) are genomic blends of components that originated at different times in different places: there was never an 'African tribe on the verge of extinction that went on to populate the world', but a single set of interbreeding Homo populations where alleles could (and did) originate anywhere"

Exactly. Couldn't agree more.

"What is the underlying assumption causing so many divergent opinions?"

It derives from the elitist attitudes that have underlain evolutionary theory since its inception. People feel a need to interpret the evidence as showing that some small group, 'superior' in some way, has replaced 'inferior' species. This in spite of the fact that if evolution proceeded in that fashion inbreeding would be a huge problem in every newly-evolved species. The fact seems to be that species do change, perhaps not 'slowly, imperceptibly', but certainly they change as genes evolve and spread through the species. Some spread widely through the species' whole geographic range. Other genes have a more limited spread. Hence we have regional 'subspecies'. One of my friends calls this 'the wave theory of evolution'.

'a population's diversity does not increase only when it is ancient, but also when it is admixed, the product of the coming together of two genetically divergent populations".

True. And that is why Y-hap c appears very diverse in India, and why Y-hap O appears very diverse in SE Asia.

"African hunter-gatherers are to a large extent the product of old admixture between 'modern' humans and archaic Africans, just as Eurasians may also be the product old admixture between 'modern' humans and archaic Eurasians, such as the Neandertals or Denisovans".

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